Landscape discontinuities influence gene flow and genetic structure in a large, vagile Australian mammal, Macropus fuliginosus

Large vagile mammals typically exhibit little genetic structuring across their range, particularly when their habitat is essentially continuous. We investigated the population genetic structure of a large vagile Australian macropodid, Macropus fuliginosus, which is continuously distributed across most of southern Australia, using nine highly polymorphic nuclear microsatellite loci. Five distinct genetic units were identified across the range, four on the mainland and one on Kangaroo Island. In addition to the predicted historic Nullarbor Plain Barrier, two unexpected mainland barriers to gene flow were identified. Both were associated with landscape discontinuities (Swan River, Flinders Ranges), which appear within the dispersal capabilities of M. fuliginosus. Typical of large vagile mammals, M. fuliginosus displays high genetic diversity (with the exception of an insular population) and weak genetic structuring (within genetic units). However, the expansion of M. fuliginosus from southwestern Australia during the Pleistocene has resulted in significantly reduced genetic diversity in eastern populations. No significant sex-biased dispersal was detected, although differences in habitat, densities and climatic conditions between the eastern and western regions of the range appear to influence dispersal with the effects of isolation by distance only evident in the west. These results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.     

Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography

Aims Building on molecular studies of widespread Australian vertebrates, we tested whether each of three widespread Australian bird species, namely the singing honeyeater, Lichenostomus virescens, spiny‐cheeked honeyeater, Acanthagenys rufogularis (Passeriformes: Meliphagidae), and black‐faced woodswallow, Artamus cinereus (Passeriformes: Artamidae), has undergone a recent (Pleistocene) range expansion across the Australian continent. We related the findings to the presence or absence of geographic variation in each species’ external phenotype and whether historical or non‐historical factors have been involved in generating variation. Methods A total of 92 specimens of the three species were collected from, as far as possible, the same localities across Australia. They were sampled for mitochondrial DNA (mtDNA) diversity in the 1041 base pairs of the ND2 gene, and these data were analysed with nucleotide diversity statistics, unrooted networks, nested clade analysis, and tests of range expansion or stability. Results Range expansions could not be rejected in any of the species in our study. Each had low, geographically unstructured nucleotide diversity. Patterns of geographic variation in the singing honeyeater's and, to a lesser extent, the black‐faced woodswallow's external phenotypes are not correlated with mtDNA diversity in ND2. Main conclusions Our study adds to the increasing number of data sets suggesting the apparent prevalence of Pleistocene population expansions in widespread Australian birds. Furthermore, it shows that observable geographic structure may evolve very quickly, in response either to environmental gradients or to historical factors that operated too recently to be detected by ND2 sequences (e.g. in the singing honeyeater). Conversely, we have shown that a species that has had a recent population expansion need not necessarily be geographically invariant. To understand fully the interplay between vicariance and dispersal in the history of widespread Australian arid‐zone birds, or between the historical and non‐historical origins of their differentiation, carefully conducted case‐by‐case molecular studies will be necessary. Only then will biogeographical patterns and the processes that led to them emerge. Study of the historical biogeography and the more recent population history of Australian arid‐zone birds has reached a point where mtDNA‐based studies, while still informative and contributing to a growing data base of such work, should be complemented with data from multiple, rapidly evolving nuclear loci.     

Phylogeography of the Alpine salamander, Salamandra atra (Salamandridae) and the influence of the Pleistocene climatic oscillations on population divergence

Fifty individuals of the endemic Alpine salamander, Salamandra atra, representing 13 populations throughout the range of the two currently recognized subspecies, atra and aurorae, were examined for sequence variation in a large portion (1050 bp) of the mitochondrial cytochrome b gene. We revealed a large number of mitochondrial DNA (mtDNA) haplotypes (10). Interpopulation sequence divergence was very low, ranging from 0 to 3.1%. The relationships among haplotypes were poorly resolved. The divergence time estimate between several mtDNA haplotypes suggested a pre-Pleistocene differentiation approximately 3 million years ago. Moreover, the impact of the Pleistocene glaciations on the phylogeographical patterns appears to have been secondary, although a somewhat reduced genetic variability was found in populations living in areas that were directly affected by the glaciation.     

Molecular population genetics of the red kangaroo (Macropus rufus): mtDNA variation

The genetic population structure of a large, wide-ranging marsupial, the red kangaroo ( Macropus rufus ) was assessed using sequence and haplotype frequency data of mitochondrial DNA (mtDNA) from locations across the species range in Australia. Results from sequence data revealed extensive haplotype diversity within the red kangaroo (32/34 sequences were unique). Sequence diversity was distributed within rather than between geographical regions across the species range. Genetic connectivity across the range of the species has therefore been maintained over the long term. On a smaller within-region scale, significant genetic structuring was evident from heterogeneity of haplotype frequencies amongst sampling sites. The geographical scale of panmictic populations differed across the continent with more restricted genetic populations occurring in areas with greater topographic and habitat complexity. We propose that these differences in area of genetic populations are the result of population responses to limiting ecological factors during drought.     

Pleistocene sea level fluctuations and the phylogeography of the dugong in Australian waters

We investigated phylogeography, demography, and population connectivity of the dugong (Dugong dugon) in Australian waters using mitochondrial control region DNA sequences from 177 Australian dugongs and 11 from elsewhere. The dugong is widespread in shallow Indo‐West Pacific waters suitable for growth of its main food, seagrass. We hypothesized that the loss of habitat and creation of a land barrier (the Torres Strait landbridge) during low sea level stands associated with Pleistocene glacial cycles have left a persisting genetic signature in the dugong. The landbridge was most recently flooded about 7,000 yr ago. Individual dugongs are capable of traveling long distances, suggesting an alternative hypothesis that there might now be little genetic differentiation across the dugong's Australian range. We demonstrated that Australian dugongs fall into two distinct maternal lineages and exhibit a phylogeographic pattern reflecting Pleistocene sea‐level fluctuations. Within each lineage, genetic structure exists, albeit at large spatial scales. We suggest that these lineages diverged following the last emergence of the Torres Strait landbridge (ca. 115 kya) and remained geographically separated until after 7 kya when passage through Torres Strait again became possible for marine animals. Evidence for population growth in the widespread lineage, especially after the last glacial maximum, was detected.     

Pleistocene origin and population history of a neoendemic alpine butterfly

Alpine environments underwent dramatic transformation during glacial–interglacial cycles, with the consequence that geographical, ecological and demographic changes of alpine populations provided the opportunity for formation of neoendemic species. Several biogeographical models have been proposed to account for the unique history of alpine populations, with different expectations of genetic divergence and speciation. The expanding alpine archipelago model proposes that alpine populations expand spatially and demographically during glacial events, dispersing between mountain ranges. Under this model, alpine populations are unlikely to diverge in isolation due to substantial interpopulation gene flow. In contrast, the alpine archipelago refuge model proposes that gene flow during glacial phases is limited and populations expand demographically during interglacial phases, increasing genetic isolation and the likelihood of speciation. We assess these models by reconstructing the evolutionary history of Colias behrii, a morphologically and ecologically distinct alpine butterfly restricted to the California Sierra Nevada. C. behrii exhibits very low genetic diversity at mitochondrial and nuclear loci, limited population structure and evidence of population expansion. C. behrii and Rocky Mountain C. meadii share identical mitochondrial haplotypes, while in contrast, nuclear data indicate common ancestry between C. behrii and Cascades Range Colias pelidne. The conflict in gene genealogies may be a result of recent expansion in North American Colias, but an isolation with migration analysis indicates that genetic patterns in C. behrii might result from differential introgression following hybridization. Based on the timing of population expansion and gene flow between mountain ranges, the expanding alpine archipelago model is supported in C. behrii.     

Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine

While many studies have documented the effect that glacial cycles have had on northern hemisphere species, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. We investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen). One thousand one hundred and sixty-six samples from across its native range were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. The contemporary distribution of east and west clades is nonoverlapping but in close proximity. Populations were estimated to have diverged in the Pleistocene around 36,000 years ago. The putative Carpentarian and Nullarbor arid barriers appear to be associated with the divergence between east and west mainland populations. Nested clade analysis indicated a signature of range expansion in the eastern region suggesting movement possibly inland and northward subsequent to the last period of aridity. The island population of Tasmania was of very recent origin, possibly since sea levels rose 16,000 years ago. Given the east-west structure, there was no congruence between morphology and recent history of this species indicating a lack of support for morphological taxa. Overall mitochondrial DNA and microsatellite variation suggest that increasing aridity and Pleistocene refugia played a role in structuring populations of the Australian magpie; however, the dispersal ability and generalist habitat requirements may have facilitated the movement of magpies into an almost contiguous modern distribution across the continent. This study supports the idea that Pleistocene aridification played an important role in structuring intraspecific variation in low latitudinal southern hemisphere avian species.     

Phylogeography and population genetics of the endangered Amazonian manatee, Trichechus inunguis Natterer, 1883 (Mammalia, Sirenia)

We used mitochondrial DNA control region sequences to examine phylogeography and population differentiation of the endangered Amazonian manatee Trichechus inunguis. We observe lack of molecular differentiation among localities and we find weak association between geographical and genetic distances. However, nested clade analysis supports restricted gene flow and/or dispersal with some long-distance dispersal. Although this species has a history of extensive hunting, genetic diversity and effective population sizes are relatively high when compared to the West Indian manatee Trichechus manatus. Patterns of mtDNA haplotype diversity in T. inunguis suggest a genetic disequilibrium most likely explained by demographic expansion resulting from secession of hunting and enforcement of conservation and protective measures. Phylogenetic analysis of T. manatus and T. inunguis haplotypes suggests that T. inunguis is nested within T. manatus, effectively making T. manatus a paraphyletic entity. Paraphyly of T. manatus and recent divergence times of T. inunguis and the three main T. manatus lineages suggest a possible need for a taxonomic re-evaluation of the western Atlantic Trichechus.     

Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history

Plethodon elongatus and P. stormi (Caudata: Plethodontidae) are Pacific Northwest endemic species which occur in northwestern California and southwestern Oregon. Studies on these salamanders have resulted in differing taxonomic conclusions, but the underlying historical hypotheses, at both inter- and intraspecific levels, have never been examined in a molecular framework. Here, representatives of 81 populations from throughout the range of both taxa are sequenced. Portions of three mitochondrial protein-coding genes (cytochrome b, NADH dehydrogenase subunit 4, and ATPase 6) were sequenced. Four haplotype groups with nonoverlapping geographical ranges were recovered in separate and combined analyses of the data. One clade corresponds to the distribution of P. stormi, while the remaining three comprise P. elongatus. Phylogenetic relationships among haplotype groups differ in separate analyses of the genes but converge on a well-supported topology, with P. elongatus and P. stormi as monophyletic sister taxa, in combined Maximum Parsimony and Maximum Likelihood analyses. Population genetic analyses of mismatch distributions and Tajima's D-statistic are consistent with range expansion for the largest clade within P. elongatus, covering the northern two-thirds of the species range. In contrast, the P. stormi haplotype clade and the P. elongatus clade from the southern third of the species range may have been relatively stable. Morphological boundaries between P. elongatus and P. stormi are largely congruent with mitochondrial DNA breaks and continued treatment as sister taxa is supported. Although mitochondrial DNA haplotype groups may reflect historical separation within P. elongatus, genetic barriers are incongruent with intraspecific patterns of morphological variation.     

Pleistocene evolutionary history of the Clouded Apollo (Parnassius mnemosyne): genetic signatures of climate cycles and a 'time-dependent' mitochondrial substitution rate

Genetic data are currently providing a large amount of new information on past distribution of species and are contributing to a new vision of Pleistocene ice ages. Nonetheless, an increasing number of studies on the 'time dependency' of mutation rates suggest that date assessments for evolutionary events of the Pleistocene might be overestimated. We analysed mitochondrial (mt) DNA (COI) sequence variation in 225 Parnassius mnemosyne individuals sampled across central and eastern Europe in order to assess (i) the existence of genetic signatures of Pleistocene climate shifts; and (ii) the timescale of demographic and evolutionary events. Our analyses reveal a phylogeographical pattern markedly influenced by the Pleistocene/Holocene climate shifts. Eastern Alpine and Balkan populations display comparatively high mtDNA diversity, suggesting multiple glacial refugia. On the other hand, three widely distributed and spatially segregated lineages occupy most of northern and eastern Europe, indicating postglacial recolonization from different refugial areas. We show that a conventional 'phylogenetic' substitution rate cannot account for the present distribution of genetic variation in this species, and we combine phylogeographical pattern and palaeoecological information in order to determine a suitable intraspecific rate through a Bayesian coalescent approach. We argue that our calibrated 'time-dependent' rate (0.096 substitutions/ million years), offers the most convincing time frame for the evolutionary events inferred from sequence data. When scaled by the new rate, estimates of divergence between Balkan and Alpine lineages point to c. 19 000 years before present (last glacial maximum), and parameters of demographic expansion for northern lineages are consistent with postglacial warming (5-11 000 years before present).     

Impact of Plio-Pleistocene arid cycling on the population history of a southwestern Australian frog

Southwestern Australia is regarded as a global biodiversity hotspot. The region contains a high number of endemic species, ranging from Gondwanan relicts to much more recently evolved plant and animal species. Myobatrachid frogs are diverse in southwestern Australia, and while we know they have speciated in situ in the southwest, we know little about the temporal and geographical patterning of speciation events. Crinia georgiana is an ideal subject to test hypotheses concerning the effect of climatic history on southwestern Australian anurans, as it is an old lineage with a broad distribution covering the entire region. We compiled an extensive phylogeographical data set based on 1085 bp of the mitochondrial gene ND2 for 68 individuals from 18 sites across the species' range. Two major genetic clades were identified which were largely confined to the high rainfall and southeast coastal biogeographical zones, respectively. The clades appear to have diverged around the Plio-Pleistocene border (1.26-1.72 million years ago), concordant with increasing intensity and frequency of arid climate cycles. Subsequent phylogeographical structure appears to have developed primarily during the Pleistocene climatic fluctuations that also have been integral in generating species diversity in the endemic southwestern Australian flora. Phylogeographical analyses identified several dispersal routes, possible refugial areas within the range of the species and also regions of secondary contact. Dispersal routes identified may now be closed to the species because of habitat destruction and salinity problems in inland regions, posing concerns about the evolutionary potential of the species in light of predicted climate change.     

A long‐standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

Aim Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long‐standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location The sub‐Saharan savanna biome of East and southern Africa. Methods Mitochondrial DNA control‐region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent‐based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr^?1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07–0.37) than for the southern lineage (0.35 Ma; 0.10–0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation‐by‐distance among populations. Main conclusions The data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer‐standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa.     

Complex population history of two Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change rather than human-mediated effects

Anopheles dirus and Anopheles baimaii are closely related species which feed on primates, particularly humans, and transmit malaria in the tropical forests of mainland Southeast Asia. Here, we report an in-depth phylogeographic picture based on 269 individuals from 21 populations from mainland Southeast Asia. Analysis of 1537 bp of mtDNA sequence revealed that the population history of A. baimaii is far more complex than previously thought. An old expansion (pre-300 kyr BP) was inferred in northern India/Bangladesh with a wave of south-eastwards expansion arriving at the Thai border (ca 135-173 kyr BP) followed by leptokurtic dispersal very recently (ca 16 kyr BP) into peninsular Thailand. The long and complex population history of these anthropophilic species suggests their expansions are not in response to the relatively recent (ca 40 kyr BP) human expansions in mainland Southeast Asia but, rather, fit well with our understanding of Pleistocene climatic change there.     

Plio‐Pleistocene diversification and genetic population structure of an endangered lizard (the Blue Mountains water skink,Eulamprus leuraensis) in south‐eastern Australia

Aim Although climatic fluctuations occurred world‐wide during the Pleistocene, the severity of glacial and drought events – and hence their influence on animal and plant biogeography – differed among regions. Many Holarctic species were forced to warmer‐climate refugia during glacial periods, leaving the genetic signature of recent expansion and gene flow among modern‐day populations. Montane south‐eastern Australia experienced less extreme glaciation, but the effects of drier and colder climatic conditions over this period on biotic distributions, and hence on the present‐day genetic structure of animal and plant populations, are poorly known. Location South‐eastern Australia. Methods The endangered Blue Mountains water skink (Eulamprus leuraensis) is a viviparous lizard known from fewer than 40 isolated small swamps at 560–1060 m elevation in south‐eastern Australia. We conducted molecular phylogenetic, dating and population genetics analyses using the mitochondrial NADH dehydrogenase 4 (ND4) of 224 individuals of E. leuraensis sampled across the species’ distribution. Results Ancient divergences in haplotype groups between lizards from the Blue Mountains and the Newnes Plateau, and strong genetic differences, even between swamps separated by only a few kilometres, suggest that the species has persisted as a series of relatively isolated populations within its current distribution for about a million years. Presumably, habitat patches similar to current‐day swamps persisted throughout glacial–interglacial cycles in this region, allowing the development of high levels of genetic structuring within and among present‐day populations. Main conclusions Our results suggest that less extreme glacial conditions occurred in the Southern Hemisphere compared with the Northern Hemisphere, allowing cold‐adapted species (such as E. leuraensis) to persist in montane areas. However, additional studies are needed before we can assemble a comprehensive view of the impact of Pleistocene climatic variation on the phylogeography of Southern Hemisphere taxa.     

Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands--a multigene approach

Phylogeography can reveal evolutionary processes driving natural genetic-geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long-term population history of a rotting-log-adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine-scale sampling combined with nested clade and coalescent-based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long-distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial-genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present-day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.     

晚更新世气候波动及长江阻隔对小麂皖南种群和大别山种群遗传分化与基因流模式的影响

通过对皖南山区和大别山区的101 个小麂的线粒体D-loop 区770 bp序列的分析,探讨了两个种群的遗传多样性、有效种群大小、历史种群动态和种群间的基因流模式。在101 个D-loop 区序列中共发现34 个单倍型,其中24 个分布在皖南种群,10 个分布在大别山种群,种群间无共享单倍型。皖南种群线粒体遗传多样性(h =0. 952,π = 0.016 8)明显高于大别山种群(h =0.734,π = 0. 007 7),雌性有效种群(N_E = 146830)亦大于大别山(N_E =19840)。通过歧点分布分析表明在更新世第四间冰期,小麂皖南种群经历过一次大规模的种群扩张事件(在约15. 7 万年前)。基因流的分析结果显示皖南种群和大别山种群间存在着明显不对等的基因流(M_{W N→DB} =0. 36;M_{DB→W N} =75. 00)。这种不对称的基因流模式可能反映出在晚更新世冰期循环中,作为天然地理屏障的长江在盛冰期和间冰期对物种扩散的阻隔能力上的差异。     

Evolutionary history of the European free-tailed bat,a tropical affinity species spanning across the Mediterranean Basin

The Mediterranean Basin is a global biodiversity hotspot, hosting a number of native species belonging to families that are found almost exclusively in tropical climates. Yet, whether or not these taxa were able to survive in the Mediterranean region during the Quaternary climatic oscillations remains unknown. Focusing on the European free-tailed bat (Tadarida teniotis), we aimed to (a) identify potential ancient populations and glacial refugia; (b) determine the post-glacial colonization routes across the Mediterranean; and (c) evaluate current population structure and demography. Mitochondrial and nuclear markers were used to understand T. teniotis evolutionary and demographic history. We show that T. teniotis is likely restricted to the Western Palearctic, with mitochondrial phylogeny suggesting a split between an Anatolian/Middle East clade and a European clade. Nuclear data pointed to three genetic populations, one of which is an isolated and highly differentiated group in the Canary Islands, another distributed across Iberia, Morocco, and France, and a third stretching from Italy to the east, with admixture following a pattern of isolation by distance. Evolutionary and demographic reconstruction supports a pre-Last Glacial Maximum (LGM) colonization of Italy and the Anatolian/Middle East, while the remaining populations were colonized from Italy after the Younger Dryas. We also found support for demographic expansion following the Iberian colonization. The results show that during the LGM T. teniotis persisted in Mediterranean refugia and has subsequently expanded to its current circum-Mediterranean range. Our findings raise questions regarding the physiological and ecological traits that enabled species with tropical affinities to survive in colder climates.     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

Lasting through the ice age: The role of the proglacial refugia in the maintenance of genetic diversity,population growth,and high dispersal rate in a widespread freshwater crustacean

1. The severe climatic changes during the Pleistocene ice ages have shaped the genetic structure and distribution of biota in Europe. We aimed to reveal in detail the genetic diversity, geographical population structure, historical and present demography, migration patterns, and the presence of possible glacial refugia within the nominative subspecies Asellus aquaticus aquaticus.
2. We analysed DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene and nuclear noncoding internal transcribed spacer II region, from populations inhabiting post-glacial Europe (from the British Isles and Scandinavia to the northern Mediterranean and Black Sea coasts).
3. The origin of the taxon, including establishment in the Dinaric Western Balkans, dates to the Middle/Late Pliocene, but most of its genetic diversity emerged during the Middle/Late Pleistocene before the Last Glacial Maximum.
4. Despite the general absence of spatial genetic structure with population growth, we discovered two different phylogeographic stories across 11 clusters revealed by a coalescent approach. Firstly, the periglacial cluster group—spatially restricted mainly to the northern Balkans, Pannonian Basin, and Pontic Region—is older and more divergent. It apparently retained a relatively stable population size during the glacial-interglacial cycles. Conversely, the proglacial cluster group—widely distributed in areas close to the glacier margins (north of the Alps, Sudetes, Carpathians) and in the Pannonian Basin—is younger and composed of closely related individuals. It originated in Pleistocene and lasted continuously through the Last Glacial Maximum in numerous high latitude refugia. This was probably due to the vast network of proglacial lakes and rivers, which played a crucial role in the maintenance of genetic diversity, population growth, and high dispersal rate.
5. The evolutionary history of A. a. aquaticus reveals unexpected patterns and is an important lesson when making predictions for other aquatic taxa. Our results suggest that we should stop perceiving the proglacial habitats as lifeless ice desert.

     

Disparate patterns of population genetic structure and population history in two sympatric penaeid shrimp species (Farfantepenaeus aztecus and Litopenaeus setiferus) in the eastern United States

Analysing the population genetic structures of sympatric species provides opportunities to compare patterns of population genetic structure and phylogeography in order to gain insight into the factors that influence the development of the observed patterns. In this study, we compared the population genetic structures and phylogeographies of brown shrimp (Farfantepenaeus aztecus) and white shrimp (Litopenaeus setiferus), two sympatric penaeid shrimp species that inhabit the waters of the eastern USA, using sequence analysis of the mitochondrial DNA control region. Brown shrimp showed no significant phylogenetic structure or population subdivision, and closely related haplotypes were geographically dispersed. Mismatch analysis indicated that brown shrimp experienced a late-Pleistocene era sudden population expansion. In contrast, white shrimp had a complex haplotype phylogeny consisting of two distinct lineages and two less well-defined sublineages, and the haplotypes and lineages were geographically structured. Mismatch analysis for white shrimp also showed evidence of sudden population expansion, albeit for each lineage separately and more recently than in the brown shrimp. These disparate patterns may have developed as a result of species-specific differences in physiological tolerances and habitat preferences that caused greater fluctuations in white shrimp population sizes and reductions in long-term effective population size relative to that of the brown shrimp, and thereby increased the susceptibility of the white shrimp populations to stochastic genetic change.